https://github.com/soedinglab/uniclust-pipeline
https://github.com/soedinglab/uniclust-pipeline
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/soedinglab/uniclust-pipeline
- Owner: soedinglab
- License: agpl-3.0
- Created: 2016-08-15T10:24:27.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2018-04-24T09:16:56.000Z (about 8 years ago)
- Last Synced: 2025-04-05T00:51:16.499Z (about 1 year ago)
- Language: Shell
- Size: 71.3 KB
- Stars: 37
- Watchers: 5
- Forks: 9
- Open Issues: 14
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Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# Uniclust Pipeline
## Setup
Make sure to install the HH-Suite3 and MMseqs2 and adjust the paths in `paths.sh`.
Also make sure that `awk, tar, pigz, cstranslate_mpi, sed, md5deep, clustalo, kalign, timeout` are all installed and available in PATH.
## Usage
To build your own databases based on the uniclust pipeline you can use the following three scripts:
* `run_main.sh`: Run Main does the clustering, builds the `uniclust30/50/90` and does the sequence enrichment of the `uniboost10/20/30` databases.
* `run_hhdatabase.sh`: Builds the `uniclust30_hhsuite` database
* `run_annotate.sh`: Builds the annotation files
Make sure to run the scripts in this order.
## LSF
The pipeline was custom build for out LSF cluster computing environment and can be submitted to the LSF with `bsub < run_mpi.sh` for example.
Please adjust the LSF parameters at the beginning of the `run_` scripts. The pipeline assumes a shared file system between the computing nodes.
## Webserver & Downloads
We provide a webserver and the Uniclust based on the UniProtKB on .